def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
self.ped_hash = load_ped_file(self.args.ped_file)
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if sample in self.ped_hash:
fields = self.ped_hash[sample]
sample_list = [i] + fields
elif len(self.ped_hash) > 0:
sys.exit("EXITING: sample %s found in the VCF but "
"not in the PED file.\n" % (sample))
else:
# if there is no ped file given, just fill in the name and
# sample_id and set the other required fields to None
sample_list = [i, None, sample]
sample_list += list(repeat(None, len(default_ped_fields) - 2))
database.insert_sample(self.c, sample_list)
def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
self.ped_hash = load_ped_file(self.args.ped_file)
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if sample in self.ped_hash:
fields = self.ped_hash[sample]
sample_list = [i] + fields
elif len(self.ped_hash) > 0:
sys.exit("EXITING: sample %s found in the VCF but "
"not in the PED file.\n" % (sample))
else:
# if there is no ped file given, just fill in the name and
# sample_id and set the other required fields to None
sample_list = [i, None, sample]
sample_list += list(repeat(None, len(default_ped_fields) - 2))
database.insert_sample(self.c, sample_list)
def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
self.ped_hash = load_ped_file(self.args.ped_file)
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if sample in self.ped_hash:
fields = self.ped_hash[sample]
sample_list = [i] + fields
elif len(self.ped_hash) > 0:
raise ValueError("Sample %s found in the VCF but "
"not in the PED file.\n" % (sample))
else:
# if there is no ped file given, just fill in the name and
# sample_id and set the other required fields to None
sample_list = [i, 0, sample, 0, 0, -9, -9]
database.insert_sample(self.c, self.metadata, sample_list)
def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
for line in open(self.args.ped_file, "r"):
field = line.strip().split("\t")
if len(field) > 1 and not field[0].startswith("#"):
ped = pedformat(field)
self.ped_hash[ped.name] = ped
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if self.ped_hash.has_key(sample):
ped = self.ped_hash[sample]
sample_list = [i, sample, ped.family, ped.paternal, ped.maternal, ped.sex, ped.phenotype, ped.ethnicity]
else:
sample_list = [i, sample, None, None, None, None, None, None]
database.insert_sample(self.c, sample_list)
def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
for line in open(self.args.ped_file, 'r'):
field = line.strip().split("\t")
if len(field) > 1 and not field[0].startswith("#"):
ped = pedformat(field)
self.ped_hash[ped.name] = ped
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if self.ped_hash.has_key(sample):
ped = self.ped_hash[sample]
sample_list = [
i, sample, ped.family, ped.paternal, ped.maternal, ped.sex,
ped.phenotype, ped.ethnicity
]
else:
sample_list = [i, sample, None, None, None, None, None, None]
database.insert_sample(self.c, sample_list)